The scaling is handled by a macro in pgfplotsticks.code.tex. You can edit this macro to implement the desired behaviour. Once the macro's been patched, you can say
\begin{axis}[scaled ticks=engineering]
\addplot {1/10000*rnd};
\end{axis}
to restrict the scaling factors to exponents that are multiples of three, the so called engineering notation:

With \addplot {1/100*rnd};:

And with \addplot {10000*rnd};:

Here's the code chunk you need to put in your preamble:
\makeatletter
\newif\ifpgfplots@scaled@x@ticks@engineering
\pgfplots@scaled@x@ticks@engineeringfalse
\newif\ifpgfplots@scaled@y@ticks@engineering
\pgfplots@scaled@y@ticks@engineeringfalse
\newif\ifpgfplots@scaled@z@ticks@engineering
\pgfplots@scaled@z@ticks@engineeringfalse
\pgfplotsset{
scaled x ticks/engineering/.code=
\pgfplots@scaled@x@ticks@engineeringtrue,
scaled y ticks/engineering/.code=
\pgfplots@scaled@y@ticks@engineeringtrue,
scaled z ticks/engineering/.code=
\pgfplots@scaled@y@ticks@engineeringtrue,
% scaled ticks=engineering % Uncomment this line if you want "engineering" to be on by default
}
\def\pgfplots@init@scaled@tick@for#1{%
\global\def\pgfplots@glob@TMPa{0}%
\expandafter\pgfplotslistcheckempty\csname pgfplots@prepared@tick@positions@major@#1\endcsname
\ifpgfplotslistempty
% we have no tick labels. Omit the tick scale label as well!
\else
\begingroup
\ifcase\csname pgfplots@scaled@ticks@#1@choice\endcsname\relax
% CASE 0 : scaled #1 ticks=false: do nothing here.
\or
% CASE 1 : scaled #1 ticks=true:
%--------------------------------
% the \pgfplots@xmin@unscaled@as@float is set just before the data
% scale transformation is initialised.
%
% The variables are empty if there is no datascale transformation.
\expandafter\let\expandafter\pgfplots@cur@min@unscaled\csname pgfplots@#1min@unscaled@as@float\endcsname
\expandafter\let\expandafter\pgfplots@cur@max@unscaled\csname pgfplots@#1max@unscaled@as@float\endcsname
%
\ifx\pgfplots@cur@min@unscaled\pgfutil@empty
\edef\pgfplots@loc@TMPa{\csname pgfplots@#1min\endcsname}%
\expandafter\pgfmathfloatparsenumber\expandafter{\pgfplots@loc@TMPa}%
\let\pgfplots@cur@min@unscaled=\pgfmathresult
\edef\pgfplots@loc@TMPa{\csname pgfplots@#1max\endcsname}%
\expandafter\pgfmathfloatparsenumber\expandafter{\pgfplots@loc@TMPa}%
\let\pgfplots@cur@max@unscaled=\pgfmathresult
\fi
%
\expandafter\pgfmathfloat@decompose@E\pgfplots@cur@min@unscaled\relax\pgfmathfloat@a@E
\expandafter\pgfmathfloat@decompose@E\pgfplots@cur@max@unscaled\relax\pgfmathfloat@b@E
\pgfplots@init@scaled@tick@normalize@exponents
\ifnum\pgfmathfloat@b@E<\pgfmathfloat@a@E
\pgfmathfloat@b@E=\pgfmathfloat@a@E
\fi
\xdef\pgfplots@glob@TMPa{\pgfplots@scale@ticks@above@exponent}%
\ifnum\pgfplots@glob@TMPa<\pgfmathfloat@b@E
% ok, scale it:
\expandafter\ifx % Check whether we're using engineering notation (restricting exponents to multiples of three)
\csname ifpgfplots@scaled@#1@ticks@engineering\expandafter\endcsname
\csname iftrue\endcsname
\divide\pgfmathfloat@b@E by 3
\multiply\pgfmathfloat@b@E by 3
\fi
\multiply\pgfmathfloat@b@E by-1
\xdef\pgfplots@glob@TMPa{\the\pgfmathfloat@b@E}%
\else
\xdef\pgfplots@glob@TMPa{\pgfplots@scale@ticks@below@exponent}%
\ifnum\pgfplots@glob@TMPa>\pgfmathfloat@b@E
% ok, scale it:
\expandafter\ifx % Check whether we're using engineering notation (restricting exponents to multiples of three)
\csname ifpgfplots@scaled@#1@ticks@engineering\expandafter\endcsname
\csname iftrue\endcsname
\advance\pgfmathfloat@b@E by -2
\divide\pgfmathfloat@b@E by 3
\multiply\pgfmathfloat@b@E by 3
\fi
\multiply\pgfmathfloat@b@E by-1
\xdef\pgfplots@glob@TMPa{\the\pgfmathfloat@b@E}%
\else
% no scaling necessary:
\xdef\pgfplots@glob@TMPa{0}%
\fi
\fi
\or
% CASE 2 : scaled #1 ticks=base 10:
%--------------------------------
\c@pgf@counta=\csname pgfplots@scaled@ticks@#1@arg\endcsname\relax
%\multiply\c@pgf@counta by-1
\xdef\pgfplots@glob@TMPa{\the\c@pgf@counta}%
\or
% CASE 3 : scaled #1 ticks=real:
%--------------------------------
\pgfmathfloatparsenumber{\csname pgfplots@scaled@ticks@#1@arg\endcsname}%
\global\let\pgfplots@glob@TMPa=\pgfmathresult
\or
% CASE 4 : scaled #1 ticks=manual:
\expandafter\global\expandafter\let\expandafter\pgfplots@glob@TMPa\csname pgfplots@scaled@ticks@#1@arg\endcsname
\fi
\endgroup
\fi
\expandafter\let\csname pgfplots@tick@scale@#1\endcsname=\pgfplots@glob@TMPa%
}
\makeatother
And here's the complete code:
\documentclass{article}
\usepackage{pgfplots}
\pgfplotsset{compat=newest}
\makeatletter
\newif\ifpgfplots@scaled@x@ticks@engineering
\pgfplots@scaled@x@ticks@engineeringfalse
\newif\ifpgfplots@scaled@y@ticks@engineering
\pgfplots@scaled@y@ticks@engineeringfalse
\newif\ifpgfplots@scaled@z@ticks@engineering
\pgfplots@scaled@z@ticks@engineeringfalse
\pgfplotsset{
scaled x ticks/engineering/.code=
\pgfplots@scaled@x@ticks@engineeringtrue,
scaled y ticks/engineering/.code=
\pgfplots@scaled@y@ticks@engineeringtrue,
scaled z ticks/engineering/.code=
\pgfplots@scaled@y@ticks@engineeringtrue,
% scaled ticks=engineering % Uncomment this line if you want "engineering" to be on by default
}
\def\pgfplots@init@scaled@tick@for#1{%
\global\def\pgfplots@glob@TMPa{0}%
\expandafter\pgfplotslistcheckempty\csname pgfplots@prepared@tick@positions@major@#1\endcsname
\ifpgfplotslistempty
% we have no tick labels. Omit the tick scale label as well!
\else
\begingroup
\ifcase\csname pgfplots@scaled@ticks@#1@choice\endcsname\relax
% CASE 0 : scaled #1 ticks=false: do nothing here.
\or
% CASE 1 : scaled #1 ticks=true:
%--------------------------------
% the \pgfplots@xmin@unscaled@as@float is set just before the data
% scale transformation is initialised.
%
% The variables are empty if there is no datascale transformation.
\expandafter\let\expandafter\pgfplots@cur@min@unscaled\csname pgfplots@#1min@unscaled@as@float\endcsname
\expandafter\let\expandafter\pgfplots@cur@max@unscaled\csname pgfplots@#1max@unscaled@as@float\endcsname
%
\ifx\pgfplots@cur@min@unscaled\pgfutil@empty
\edef\pgfplots@loc@TMPa{\csname pgfplots@#1min\endcsname}%
\expandafter\pgfmathfloatparsenumber\expandafter{\pgfplots@loc@TMPa}%
\let\pgfplots@cur@min@unscaled=\pgfmathresult
\edef\pgfplots@loc@TMPa{\csname pgfplots@#1max\endcsname}%
\expandafter\pgfmathfloatparsenumber\expandafter{\pgfplots@loc@TMPa}%
\let\pgfplots@cur@max@unscaled=\pgfmathresult
\fi
%
\expandafter\pgfmathfloat@decompose@E\pgfplots@cur@min@unscaled\relax\pgfmathfloat@a@E
\expandafter\pgfmathfloat@decompose@E\pgfplots@cur@max@unscaled\relax\pgfmathfloat@b@E
\pgfplots@init@scaled@tick@normalize@exponents
\ifnum\pgfmathfloat@b@E<\pgfmathfloat@a@E
\pgfmathfloat@b@E=\pgfmathfloat@a@E
\fi
\xdef\pgfplots@glob@TMPa{\pgfplots@scale@ticks@above@exponent}%
\ifnum\pgfplots@glob@TMPa<\pgfmathfloat@b@E
% ok, scale it:
\expandafter\ifx % Check whether we're using engineering notation (restricting exponents to multiples of three)
\csname ifpgfplots@scaled@#1@ticks@engineering\expandafter\endcsname
\csname iftrue\endcsname
\divide\pgfmathfloat@b@E by 3
\multiply\pgfmathfloat@b@E by 3
\fi
\multiply\pgfmathfloat@b@E by-1
\xdef\pgfplots@glob@TMPa{\the\pgfmathfloat@b@E}%
\else
\xdef\pgfplots@glob@TMPa{\pgfplots@scale@ticks@below@exponent}%
\ifnum\pgfplots@glob@TMPa>\pgfmathfloat@b@E
% ok, scale it:
\expandafter\ifx % Check whether we're using engineering notation (restricting exponents to multiples of three)
\csname ifpgfplots@scaled@#1@ticks@engineering\expandafter\endcsname
\csname iftrue\endcsname
\advance\pgfmathfloat@b@E by -2
\divide\pgfmathfloat@b@E by 3
\multiply\pgfmathfloat@b@E by 3
\fi
\multiply\pgfmathfloat@b@E by-1
\xdef\pgfplots@glob@TMPa{\the\pgfmathfloat@b@E}%
\else
% no scaling necessary:
\xdef\pgfplots@glob@TMPa{0}%
\fi
\fi
\or
% CASE 2 : scaled #1 ticks=base 10:
%--------------------------------
\c@pgf@counta=\csname pgfplots@scaled@ticks@#1@arg\endcsname\relax
%\multiply\c@pgf@counta by-1
\xdef\pgfplots@glob@TMPa{\the\c@pgf@counta}%
\or
% CASE 3 : scaled #1 ticks=real:
%--------------------------------
\pgfmathfloatparsenumber{\csname pgfplots@scaled@ticks@#1@arg\endcsname}%
\global\let\pgfplots@glob@TMPa=\pgfmathresult
\or
% CASE 4 : scaled #1 ticks=manual:
\expandafter\global\expandafter\let\expandafter\pgfplots@glob@TMPa\csname pgfplots@scaled@ticks@#1@arg\endcsname
\fi
\endgroup
\fi
\expandafter\let\csname pgfplots@tick@scale@#1\endcsname=\pgfplots@glob@TMPa%
}
\makeatother
\begin{document}
\pgfmathsetseed{1}
\begin{tikzpicture}
\begin{axis}[height=4cm, width=8cm]
\addplot {1/100000*x};
\end{axis}
\end{tikzpicture}
\end{document}